What happens to the microbiome – the countless bacteria that live inside the gut – when you stop eating dairy, processed sugars and carbs?

This is what doctors at the Amos Center for Food, Body & Mind at Johns Hopkins Bayview Medical Center want to know.Some of their patients who have irritable bowel syndrome (characterized by constipation, diarrhea, and nausea, it also can include anxiety or depression) have reported that they have been doing better after changing to a Paleo diet.

To help find out why, Kimberly Harer, M.D., gastroenterology fellow at the Center, designed a short-term study.I recently interviewed Harer and her colleague, epidemiologist Noel Mueller, Ph.D., for Breakthrough, a publication of the Center for Innovative Medicine at Johns Hopkins.

For two weeks, she says, 40 patients with IBS will be randomly assigned to eat either a Paleo diet or a standard, healthful diet.Harer and Mueller will be looking at many things in these study participants, including “how the diet affects their GI symptoms, their quality of life, their vitality,” says Harer.In people who have been experiencing anxiety or depression, the investigators will look for changes in these symptoms, as well.They will study blood samples and patient responses to questionnaires about their health, and then, looking at the bacteria in stool specimens, the scientists will analyze the gut “microbiome” before and after.

Let’s just take a moment to reflect on the concept – still fairly new in research – of a microbiome: It’s a small ecosystem made up of bacteria; this is more complex than it sounds.Just as the earth has its own ecosystems – tundra, tropical rainforests, grasslands – your body has them, too.Except instead of plants, these microbiomes are populated by bacteria: dozens of them, picky little cliques that only thrive in one particular spot. For example, the bacteria on the inside of your elbow are different from the bacteria on your face – and even on your face, the bacteria on the bridge of your nose are different from the bacteria between your nose and mouth; and those bacteria are different from bacteria on your chin.

But the gut takes it to another level; it is the microbial mother lode.In numbers alone, it’s intimidating.“There are trillions of microbiota (tiny habitats) in the gut,” says Mueller.And get this:All of those bacteria in all those micro-habitats have their own genes and their own genomes, which scientists now know how to sequence.“There are 100 to one more microbial genes than in your own human genome.”

This is why scientists at the Amos Center are convinced that the microbiome has an important influence on our health.It’s not just numbers, it’s sheer mass:All those bacteria that live inside our gut, if you somehow got them all together in one lump, would weigh and take up about as much space as your brain – three or four pounds.Trying to get a handle on that would be overwhelming without sophisticated computers and software, sequencing technology, and bioinformatics tools that allow scientists to recognize patterns and identify gene signatures.

Because the study of the gut’s microbiome is still so new, nobody is sure what it’s supposed to look like, and how the gut flora relates to symptoms.“Maybe we won’t ever be able to define what is the normal gut microbiome,” says Mueller.“Normal might be different for everybody.”

Even in identical twins, Mueller continues, the bacteria in the gut can be very different.It is not unheard of for one twin to have a normal weight, and one to be obese.

Already, at many hospitals gut doctors are waging war with bacteria, successfully treating patients who suffer debilitating diarrhea from recurrent Clostridium difficile (C.diff) colitis with fecal microbiota transplants.Basically, uninfected fecal material from a relative with healthy gut bacteria is inserted into the patient’s colon, the good bacteria overwhelm the bad bacteria and the C.diff. is conquered.

In mice, Mueller notes, scientists have found that if they take the microbiota from the fecal sample of an obese individual and inject it into a germ-free mouse, that germ-free mouse will start to become overweight, too.“The phenotype of obesity can be replicated just through the sharing of bacteria,” he says.There is a lot of evidence to suggest that gut bacteria play a huge role in diseases of the metabolism – which also suggests that if these bacteria can be changed, there is great potential to improve someone’s health.

In this study, says Harer, “we will look at the microbiome at three different time points.First, the baseline, before the diet changes; then, after the Paleo or study diet.”And then one more time: after participants go back to eating whatever they used to eat for four weeks.Blood samples will be taken after that four-week period, as well, and patients will fill out questionnaires to report any change in their symptoms.

“If there are differences in the blood and the stool samples, it will be interesting to see if those correlate with changes in their symptoms,” says Harer.“And we are very interested to see whether reverting back to their old diet causes the former symptoms to come back, or whether there are lasting changes.”

Certain families of bacteria thrive on a diet full of macaroni and cheese, soda, and ham sandwiches.Entirely different bacteria could show up if that diet changes to lean meat, nuts, berries, and veggies.Which raises another question: If someone gets better with the Paleo diet, “what part is the beneficial part?Is it the lower carbs?Is it the increase in plants, or in protein content?Is it cutting out gluten?”Or is it some new, beneficial bacteria that have taken precedence in the gut?

It’s important to remember that “the microbiome is just part of the study,” Harer continues.“The question is, does this diet improve symptoms in IBS patients?Unfortunately, there is a huge unmet need in these patients, because there are few effective treatments.”

Many people who have IBS are not treated very thoughtfully; they get laxatives for constipation, medicine for diarrhea, and often the symptoms don’t go away because the underlying cause is still there.The Amos Center takes a team approach with gastroenterologists, allergists and immunologists, psychiatrists, nutritionists, and scientists.Sometimes, Harer says, people who come to the Center are “frustrated, at the end of their rope sometimes when they come to see us.We use everyone’s input to treat them holistically, and also to try new things.”

One of these new things is a diet so simple that – as the commercials put it – “a caveman could do it.”If the Paleo diet does indeed help make people with IBS feel better, understanding why it works at gut level is something we’re only beginning to have the scientific knowledge and tools to decipher.

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Medicine wears off.If you take a pill, its benefit might last for 12 or even 24 hours, and then you have to take another one.The same holds true for acupuncture. Although administered differently – inserting very thin needles through your skin at strategic points – its effects tend to fade just as quickly.

There’s one big difference:Most people who get acupuncture only have it once or twice a week, at most. Imagine if you had an antibiotic that worked, and you only took it once a week.

Courtesy of Johns Hopkins Medicine

Jiande Chen, Ph.D., a Johns Hopkins biomedical engineer working with the Amos Food, Body, and Mind Center, is about to change this.I interviewed him recently for Breakthrough, a magazine for the Johns Hopkins Center for Innovative Medicine.

Chen specializes in the pathophysiology of gastrointestinal motility – how food moves through your body — as well as diabetes and obesity.He is particularly interested in electrical therapies that stimulate the nerves involved in gut function, and now he has developed a novel device for patients to use at home that provides “transcutaneous electrical stimulation” similar to the effect of acupuncture.

In other words, he’s developed a smart watch for acupuncture.

Requiring only a watch battery, it delivers a painless, noninvasive dose of electric current that penetrates as deeply and precisely as one of those long, thin needles.But patients can administer it themselves, at home, after every meal.

It’s safe, DIY home acupuncture, and it might significantly change the way people with certain conditions, starting with gastroparesis, find relief.

In gastroparesis, the stomach is slow to empty.Food lingers because the muscles that should move it along to the gut – squeezing it like toothpaste through a tube – are either damaged or weak.One big cause is diabetes.The condition can be miserable and can include decreased appetite, heartburn, nausea, vomiting, bloating, anxiety, and discomfort.Symptoms are usually treated with medicine and dietary changes, but in a recent study, Hopkins scientists showed that acupuncture can also help relieve symptoms.

Now, let’s switch for a moment and look at gastroparesis as an acupuncturist would. In traditional Chinese medicine, a complex system of healing more than 5,000 years old, practitioners believe our vital energy, called “qi” (pronounced “chee”), flows through the body along 12 pathways, called meridians.Each meridian involves a different organ system.

When all is well, the qi flows smoothly; but when there is an imbalance somewhere, the flow is blocked or hindered, and that’s how disease can begin.The needles inserted during acupuncture are designed to restore this balance.Gastroparesis might be called “food stagnation,” or “liver and spleen disharmony” in Chinese medicine, but the basic problem would be the same: food not moving through the digestive tract.The liver is supposed to ensure that everything – digestion as well as emotions – flows smoothly.When this flow is blocked, it weakens the spleen, which is in charge of digestion.

Acupuncture stimulates nerves – in this case, the vagus nerve, which reaches all the way from the brain down through the esophagus, heart, and lungs, down to the abdomen, and controls many things, including digestion.It also stimulates blood flow by dilating blood vessels and causes the body to release endorphins, natural painkillers.

In someone with gastroparesis, acupuncture sends a signal to the brain via the vagus nerve, telling the stomach to work better.

Chen’s device works by neuromodulation, using electrical stimulation to change how nerve cells interact. In painstaking research, he has determined the precise levels needed to produce a beneficial change in the function of the nerves – how much energy to release, the speed of the electrical signal, the width of the pulse.

That precision “is one difference between our method and traditional Chinese medicine.”Another is frequency:“It would be very expensive to do traditional acupuncture two or three times a day, but with this device, you are just putting an electrode at the acupuncture points.You could do it after every meal.”

There are two key placement points:One is the wrist, “which is very good for treating symptoms like nausea, vomiting, and motion sickness.That wrist acupuncture point is very close to the medial nerve.” The other is about 5 centimeters below the knee, a place called “stomach point number 36” in acupuncture.“This is very close to the perineal nerve,” and stimulation here “is known to enhance the autonomic nerve function, which helps empty the stomach and improves the digestive process.”

Basically, Chen explains, “We combined modern neuromodulation theory with traditional Chinese acupuncture.”This is just the kind of project its leaders envisioned when the Amos Food, Body, and Mind center began a year ago: blending Eastern medicine with state-of-the-art technology in a holistic, whole-body approach to improving health.

The device has not yet received FDA approval and it doesn’t work for everyone, Chen notes, “but our results of early studies are very exciting.”In related work, Chen plans to see whether the device can help improve symptoms in patients with scleroderma and whether it can help reduce the appetite in people with obesity.

Imagine:John Wayne in True Grit, charging bad guys on horseback, with the reins in his teeth, a Colt revolver in one hand and a Winchester rifle in the other, and suddenly, he veers off and heads for the woods. He’s acutely regretting that cup of coffee he had back at the campfire.

Well, that didn’t happen, because he’s John Wayne.But it certainly might happen to us lesser mortals.In fact, this laxative effect is a known consequence — or, hey! It’s a benefit, depending on how you look at it – of drinking coffee.The effect can happen in as little as four minutes, according to an English study published in the journal, Gut.

Why does coffee make some people need to poop?Several reasons.It’s not the caffeine (decaf can produce the same effect), and it’s not the heat of the beverage; the English scientists tested drinking hot water in the same group of study participants, and nothing happened.Out of 14 people studied (12 men, two women), eight of those who drank black, unsweetened coffee needed to move their bowels.The coffee sped up the gut’s motility – movement of food through the digestive tract, using a series of muscle contractions called peristalsis – in the eight responders, but not in the others.“The increase in rectosigmoid motility induced by coffee lasted at least 30 minutes,” the scientists reported.“These results suggest that drinking coffee can stimulate a motor response of the distal colon in some normal people.”

The fact that this happened so darned fast, the researchers speculated, doesn’t mean that coffee actually rockets through the system.Instead, “we suspect that coffee may induce a ‘gastrocolonic response’ by acting on epithelial receptors in the stomach or small bowel.”This might be activated by nerves or hormones in the GI tract; also, they added, “coffee has been shown to promote release of gastrin, which can increase colonic … motor activity.”So for some people, coffee shifts the gut into temporary fast-forward mode.

Why Does Coffee Make You Poop?Coffee is a great way to wake you up, and it’s also a great way to keep you regular. What’s so special about coffee that it makes you poop?—–For a collection of all our videos, check out TestTube Video!

What else does it do?I am fortunate to be married to an excellent gastroenterologist, Mark Worthington, M.D., formerly on the medical faculty at the University of Virginia and Johns Hopkins and now in private practice in Arizona.“Basically, coffee causes a net secretion of fluid into the small intestine,” he says.“For most people, the colon takes up the slack – it sucks up the extra water – but it gets activated in the process.For some people, coffee actually leads to diarrhea because the colon can’t handle it all.”People who particularly have trouble with coffee, he adds, are those with colitis (inflammation of the colon).Also: “coffee sweeteners, such as Stevia, can cause diarrhea in some people.”If you add a lot of dairy to your coffee, and dairy products are difficult for you, this might make coffee a bit of a digestive challenge, as well.

Is that it?Well, no, there’s the acid.Coffee is loaded with a phenol called “chlorogenic acid,” and – again, not in everyone – for those of us who lack cast-iron stomachs and are already prone to acid reflux, or for people who drink coffee on an empty stomach, the acid can irritate the stomach lining.This is called gastritis, and it can result in heartburn, hiccups, pain in the belly, nausea, and can even make you throw up if you don’t get some food in there to help combat the acid.Caffeine itself – let’s face it, the major reason we drink coffee – also can cause the stomach to pump out more acid.

Note:Don’t think I’m anti-coffee.I’m not at all.Coffee also does a lot of good things, including help lower your risk for Alzheimer’s disease, which I will talk about in some future post.This is not that post.

Good news for your tummy:If coffee starts your day off with an upset stomach or gives you the rumblies, don’t despair:You are not alone.In fact, there are so many people with this problem that gut-friendly coffees – with more available all the time – have been developed just for you.

Which is good news.However, if you’re one of those susceptible to coffee’s Number Two side effect – no matter how gentle or organic or gourmet your coffee may be — you’ll still probably have to poop after you drink it.

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Ever had a gut feeling? Felt butterflies in your stomach? Maybe gotten a little crampy or needed to make an emergency trip to the bathroom during times of stress?

Now, let’s look at this from the other end, so to speak: Maybe you’ve been feeling anxious or depressed. Maybe you feel bad, and you don’t know why. Maybe something in your diet is making you feel this way.

Maybe what you eat is making you sick.

There is an intimate, intricate link between the brain and the gut that scientists are just beginning to understand. Questions are being asked and investigated that, frankly, nobody thought of even a few years ago, because the connections weren’t there yet. That is changing.

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Here are some fun facts you should know about what scientists call the gut-brain axis:

You have as many neurons (nerve cells) in your gut as you do in your spinal cord.

These intestinal nerve cells crank out 90 percent of your body’s serotonin and half of its dopamine. Both of these powerful neurotransmitters help the mind stay calm and focused and are natural anti-depressants.

If you go to a doctor for irritable bowel symptoms (such as alternating diarrhea and constipation) or dyspepsia (uncomfortable fullness or pain in the upper abdomen, heartburn, or other digestive problems), you are likely to be prescribed one of the same drugs used to treat anxiety or depression. Doctors don’t really understand why these “brain” drugs work on the gut, but they know that they help make symptoms better.

As many as 40 percent of people who go to the doctor with gastrointestinal problems suffer from irritable bowel syndrome and gastroparesis (the stomach muscles or the nerves that drive them stop working, and food doesn’t move out of the stomach the way it should) – conditions that involve the enteric nervous system. This is the massive highway of nerve cells lining the muscular walls of your esophagus, stomach, intestines, and rectum.

These nerves control peristalis, the conveyor-belt series of muscle contractions — think of toothpaste being squeezed through a tube — essential for swallowing, for digestion, absorption of food, and for pooping (literally, movement of the bowels).

These enteric nerves also affect immune responses and inflammation.

Changes in our mood can also affect everything in the gut.

Is there really a food-mood connection? Here’s a good example: An estimated 1 in 133 Americans have celiac disease, an autoimmune disease in which the body attacks the small intestine (this can be diagnosed with a blood test). The culprit is gluten, which is in wheat. If you have celiac disease and you don’t change your diet, and you get an upper endoscopy, if you are lucky, it will likely show a telltale “cobblestoning” of the small intestine – damage to the villi, tiny, fingerlike oars that help the small intestine absorb the nutrients in your food. This damage is reversible. Within a few weeks of going gluten-free, these little dudes come back and your small intestine can do its job again. If you are not lucky, a biopsy to the small intestine will show that the celiac disease has caused cancer, and this is not good.

Am I saying you have celiac disease if bread gives you a belly ache? No, but bear with me: One, a lot of people test negative for the disease itself, but notice they feel bad when they eat bread or pasta. They feel bloated, maybe a little cranky; maybe they also get headaches. They also feel better when they eliminate gluten from their diet. They may have gluten intolerance, which is not the same as celiac disease, but responds well to a change in diet. Two: People with celiac disease who give up gluten notice a lot of other changes in their lives. They may put on muscle mass, because their body was starving from the inside; no matter how much they ate, they weren’t absorbing the good nutrients, because their small intestines didn’t function right. They also tend to realize, with great surprise, that they have felt bad for years; they just didn’t know why. And here’s the kicker: Their mood improves.

Celiac disease can cause depression, irritability, and anxiety, but can get better with a diet change.

What I want you to think about is this: If it can happen with one gut disease, it can happen in other problems involving the gut and/or diet. Food affects mood. Maybe you have a food allergy or intolerance that you didn’t know about. The nerve cells in the gut affect your mood. It’s the opposite of those ads for Las Vegas: What happens in the gut does not necessarily stay in the gut.

Food, Body & Mind

“The gut has its own brain,” says Pankaj “Jay” Pasricha, M.D., gastroenterologist and neuroscientist, director of the Center for Digestive Diseases at Johns Hopkins Bayview Medical Center, and co-director of the new Johns Hopkins Food, Body & Mind Center. At this center, the science is a fusion: it’s Gastroenterology, Neuroscience, Microbiology, Immunology, and Psychiatry. They’ve got a bunch of doctors and scientists working together to figure out just how important a role the gut plays in diseases that seem like they wouldn’t trouble the intestines – diabetes, heart disease, depression, anxiety, even cancer.

I have interviewed Jay Pasricha several times for the Johns Hopkins Center for Innovative Medicine’s magazine, Breakthrough. At the Center, he says, many of their patients come to them by way of a rather long road. Basically, they’ve been through a lot — medicines that may not have worked, for example, or doctors who may have addressed one of their problems without realizing the whole body was involved. Pasricha told me that his research involves multiple aspects of the gut-brain axis. He is very interested in the pancreas, in exploring “how the gut can be a signal that drives metabolic disease,” he says, and “finding the mechanism by which gastric bypass surgery relieves insulin resistance and diabetes.” Pasricha has also shown in mouse models of diabetes that there is remodeling of the enteric nerves that help control insulin production; he believes that a new approach to treating diabetes — by changing the way the nerves signal to each other — may be on the horizon.

Enteric nerves

Exactly how the brain in the gut relates to the “big brain” is what Pasricha and his colleagues are working hard to find out, testing the potential of never-before-recognized molecular targets for treatment of nausea, abdominal pain, and other symptoms that may arise when mind-gut pathways go awry. “The treatment of motility disorders (like irritable bowel disease and gastroparesis) really requires the art as well as the science of medicine, because every patient responds differently,” notes Pasricha. “In fact, there are very few effective treatments, and what works for one person might not be very helpful for another,” which is why he believes that entirely new avenues of treatment might make a huge difference in care.

But better treatment for motility disorders is most likely just the tip of the gut-brain iceberg, Pasricha believes. The enteric nerves almost certainly play a role in obesity, diabetes, in pancreatitis; they may even be involved in Alzheimer’s disease, some forms of cancer, and other diseases that aren’t usually thought of as relating to the gut.

These nerves are involved in immune responses, he explains, “and this process, called neurogenic inflammation, is a problem in many disabling diseases.” Signals from the enteric nervous system affect metabolism in the brain, liver, and elsewhere. “The bigger picture here is enormous.”

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